sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2013-10-14
| Name: | Serine/threonine-protein kinase pim-1 |
|---|---|
| ID: | PIM1_HUMAN |
| AC: | P11309 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.860 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.434 | 556.875 |
| % Hydrophobic | % Polar |
|---|---|
| 64.24 | 35.76 |
| According to VolSite | |
| HET Code: | 2HX |
|---|---|
| Formula: | C23H24F3N5O2 |
| Molecular weight: | 459.464 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.32 % |
| Polar Surface area: | 107.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -18.7989 | 37.7232 | -2.71409 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| C14 | CB | LEU- 44 | 3.57 | 0 | Hydrophobic |
| F32 | CD1 | LEU- 44 | 3.26 | 0 | Hydrophobic |
| C8 | CB | PHE- 49 | 4.19 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 52 | 4.21 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 52 | 4.3 | 0 | Hydrophobic |
| F32 | CB | ALA- 65 | 4.4 | 0 | Hydrophobic |
| C19 | CB | ALA- 65 | 3.69 | 0 | Hydrophobic |
| N10 | NZ | LYS- 67 | 2.83 | 170.28 | H-Bond (Protein Donor) |
| C18 | CG1 | ILE- 104 | 3.8 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 104 | 3.61 | 0 | Hydrophobic |
| C18 | CB | LEU- 120 | 4 | 0 | Hydrophobic |
| F24 | CG | ARG- 122 | 3.57 | 0 | Hydrophobic |
| F32 | CD | ARG- 122 | 3.44 | 0 | Hydrophobic |
| F24 | CG2 | VAL- 126 | 4.09 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 126 | 3.88 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 126 | 3.54 | 0 | Hydrophobic |
| N25 | OD1 | ASP- 128 | 2.59 | 150.57 | H-Bond (Ligand Donor) |
| N25 | OD1 | ASP- 128 | 2.59 | 0 | Ionic (Ligand Cationic) |
| F31 | CB | ASP- 128 | 4.27 | 0 | Hydrophobic |
| N25 | O | GLU- 171 | 2.78 | 153.42 | H-Bond (Ligand Donor) |
| F31 | CD2 | LEU- 174 | 3.55 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 174 | 3.22 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 185 | 3.8 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 185 | 3.88 | 0 | Hydrophobic |
| C18 | CG2 | ILE- 185 | 4.08 | 0 | Hydrophobic |
| F31 | CD1 | ILE- 185 | 3.45 | 0 | Hydrophobic |
| C8 | CB | ASP- 186 | 4.02 | 0 | Hydrophobic |
